Hi the team,
I have probably misunderstood how to make CatVariants working - probably the assumedSorted function that I don't really understand in the help.
I used the following command line to merge two g.vcf obtained from two runs for the same sample :
java -cp /usr/local/lib/GATK/GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants -R hg19_min_oldM.fa -V sample_1.g.vcf -V sample_2.g.vcf -out sample_combine.g.vcf -assumeSorted
It worked without error message - that is already not so good....
But when I tried to use this combined g.vcf during the genotyping step, I obtained this error :
ERROR MESSAGE: Input file must have contiguous chromosomes. Saw feature chr1:65510-65625 followed later by chrY:59340274-59340374 and then chr1:65510-65625, for input source: sample_combine.g.vcf -assumeSorted
And effectively, if I grep the gulty positions, I saw that the two g.vcf have been put underneath one another :
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample
chr1 65510 . T . . END=65625 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
[...] all the variants
chrY 59340274 . T . . END=59340374 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
chr1 65510 . T . . END=65625 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
[...] all the variants again
What I wanted was a real "mix" for each position, and I neither know how to do, and if it is only possible ?
Thanks by advance,
BPR